What exactly does the "Use 3D Viewport" rendering option do?
As far as I can tell this is for use together with Local Camera feature of a viewport, or the now possible multi-window workflows.
Using local camera you can have any viewport display an arbitrary camera other than the one defined as active camera in the Scene tab of the Properties Editor.

Rendering from such viewport would potentially lead to unexpected behavior, as the produced image would not match the view angle currently visible in a 3D view, since by default Blender would be rendering the scene active camera, rather than the one you would be seeing through.
With Use 3D Viewport option checked you render what is actually displayed in the current 3D View the command originated from, using context as deps-graph source, regardless of default scene settings.
I suspect this possibly overrides other settings as well, like say rendering from another Blender window from the same session that has a different active view layer from the scene default one, or different visibility or collection states.